Variant report

Variant	rs2242188
Chromosome Location	chr1:223976195-223976196
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223974924..223977423-chr1:223981900..223984346,2	MCF-7	breast:
2	chr1:223975312..223979153-chr1:224030482..224035909,7	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1003061	0.84[ASN][1000 genomes]
rs1153927	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153929	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153934	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153936	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153937	0.93[EUR][1000 genomes]
rs1153938	0.93[EUR][1000 genomes]
rs1153943	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1153947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1153949	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1153971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1153973	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222120	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1222146	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222156	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1621129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1629850	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16842270	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16842321	0.91[ASW][hapmap];1.00[CEU][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1981171	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1982610	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1982613	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28370163	0.89[EUR][1000 genomes]
rs28370164	0.89[EUR][1000 genomes]
rs28370167	0.89[EUR][1000 genomes]
rs28370172	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653457	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56329085	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56918361	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59104475	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59196624	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60131749	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60164080	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60739082	0.83[ASN][1000 genomes]
rs6604726	0.81[ASN][1000 genomes]
rs6661816	0.85[ASN][1000 genomes]
rs6675712	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687003	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694214	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72749554	0.90[EUR][1000 genomes]
rs72749569	0.94[EUR][1000 genomes]
rs72749588	0.86[ASN][1000 genomes]
rs737066	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs750873	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7536779	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs898878	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
6	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
11	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas
14	chr1:223963400-223983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:223964000-223985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:223964200-223980000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:223964400-223977200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:223964400-223979600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:223964600-223976800	Weak transcription	Stomach Mucosa	stomach
21	chr1:223964600-223977000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:223965400-223977200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:223965400-223983800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:223966400-223976200	Weak transcription	NHEK	skin
25	chr1:223966600-223983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:223967800-223979800	Weak transcription	Fetal Brain Male	brain
27	chr1:223968400-223979800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:223968400-223984000	Weak transcription	Colonic Mucosa	Colon
29	chr1:223968600-223983000	Weak transcription	Small Intestine	intestine
30	chr1:223969000-223983400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:223969200-223983400	Weak transcription	HepG2	liver
32	chr1:223969800-223995200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223970000-223995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:223970200-223977400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:223970200-223977400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:223970600-223976200	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:223970600-223982000	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:223970600-223990400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:223971200-223979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:223971200-223983400	Weak transcription	Esophagus	oesophagus
41	chr1:223971400-223976600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:223971400-223983400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:223971400-223985200	Weak transcription	Gastric	stomach
44	chr1:223971400-223985800	Weak transcription	Aorta	Aorta
45	chr1:223972000-223976400	Weak transcription	Osteobl	bone
46	chr1:223972000-223976600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:223972000-223983400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:223972000-223983600	Weak transcription	Right Ventricle	heart
49	chr1:223972000-223985400	Weak transcription	HMEC	breast
50	chr1:223972200-223976200	Weak transcription	Fetal Heart	heart

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